Incidental Mutation 'R7305:Smpd4'
ID 567275
Institutional Source Beutler Lab
Gene Symbol Smpd4
Ensembl Gene ENSMUSG00000005899
Gene Name sphingomyelin phosphodiesterase 4
Synonyms 4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)
MMRRC Submission 045407-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.098) question?
Stock # R7305 (G1)
Quality Score 225.009
Status Not validated
Chromosome 16
Chromosomal Location 17437218-17462692 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 17459647 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 656 (I656N)
Ref Sequence ENSEMBL: ENSMUSP00000006053 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000056962] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000165363] [ENSMUST00000182117] [ENSMUST00000182344] [ENSMUST00000182368] [ENSMUST00000231436] [ENSMUST00000231627] [ENSMUST00000231722] [ENSMUST00000231792] [ENSMUST00000232021] [ENSMUST00000232116] [ENSMUST00000232271]
AlphaFold Q6ZPR5
Predicted Effect probably damaging
Transcript: ENSMUST00000006053
AA Change: I656N

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: I656N

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 768 N/A PFAM
transmembrane domain 769 791 N/A INTRINSIC
transmembrane domain 798 815 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000056962
SMART Domains Protein: ENSMUSP00000049541
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
low complexity region 12 34 N/A INTRINSIC
Pfam:CCDC92 50 105 4.1e-24 PFAM
low complexity region 154 164 N/A INTRINSIC
Pfam:CCDC74_C 209 326 1.4e-49 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000090159
AA Change: I640N

PolyPhen 2 Score 0.794 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: I640N

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 288 7.4e-177 PFAM
Pfam:mit_SMPDase 287 752 9.4e-259 PFAM
transmembrane domain 753 775 N/A INTRINSIC
transmembrane domain 782 799 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000163476
AA Change: I627N

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: I627N

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 289 6.2e-177 PFAM
Pfam:mit_SMPDase 285 739 9.8e-266 PFAM
transmembrane domain 740 762 N/A INTRINSIC
transmembrane domain 769 786 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000165363
AA Change: I626N

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: I626N

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 289 6.2e-177 PFAM
Pfam:mit_SMPDase 285 738 4.1e-262 PFAM
transmembrane domain 739 761 N/A INTRINSIC
transmembrane domain 768 785 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000182117
SMART Domains Protein: ENSMUSP00000138657
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
low complexity region 1 21 N/A INTRINSIC
Pfam:CCDC92 36 97 2e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000182344
SMART Domains Protein: ENSMUSP00000138131
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
Pfam:CCDC92 18 79 1.4e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000182368
SMART Domains Protein: ENSMUSP00000138262
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
low complexity region 12 34 N/A INTRINSIC
Pfam:CCDC92 49 110 2.9e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000182671
Predicted Effect probably benign
Transcript: ENSMUST00000182976
Predicted Effect probably benign
Transcript: ENSMUST00000183279
Predicted Effect possibly damaging
Transcript: ENSMUST00000231436
AA Change: I627N

PolyPhen 2 Score 0.851 (Sensitivity: 0.83; Specificity: 0.93)
Predicted Effect probably benign
Transcript: ENSMUST00000231627
Predicted Effect probably benign
Transcript: ENSMUST00000231722
Predicted Effect possibly damaging
Transcript: ENSMUST00000231792
AA Change: I406N

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)
Predicted Effect possibly damaging
Transcript: ENSMUST00000232021
AA Change: I554N

PolyPhen 2 Score 0.597 (Sensitivity: 0.87; Specificity: 0.91)
Predicted Effect probably benign
Transcript: ENSMUST00000232116
Predicted Effect possibly damaging
Transcript: ENSMUST00000232271
AA Change: I332N

PolyPhen 2 Score 0.921 (Sensitivity: 0.81; Specificity: 0.94)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Sphingomyelinases (EC 3.1.4.12), such as SMPD4, catalyze the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (Krut et al., 2006 [PubMed 16517606]).[supplied by OMIM, Mar 2008]
Allele List at MGI
Other mutations in this stock
Total: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd16b A T 2: 181,135,209 (GRCm39) D37V possibly damaging Het
Ankhd1 A G 18: 36,765,258 (GRCm39) D87G Het
Ankrd31 A G 13: 97,015,479 (GRCm39) S1583G probably damaging Het
Ankub1 T C 3: 57,599,938 (GRCm39) probably benign Het
Apba3 A G 10: 81,107,067 (GRCm39) D264G probably damaging Het
Armh3 A T 19: 45,880,560 (GRCm39) M508K probably benign Het
Asap1 G A 15: 64,002,099 (GRCm39) T404M probably damaging Het
Cnot3 A T 7: 3,648,479 (GRCm39) probably benign Het
Cxxc1 A G 18: 74,352,467 (GRCm39) Y349C probably benign Het
Cyfip1 AGTGT AGT 7: 55,577,937 (GRCm39) probably null Het
Cyp3a57 A G 5: 145,307,795 (GRCm39) I184V probably benign Het
D130052B06Rik GTCTACACTGTCCTGCACAGGTGACCCATCTACCCCGTCCTATCCTGGCGACCCATCTACACTGTCCTG GTCTACACTGTCCTG 11: 33,573,355 (GRCm39) probably null Het
Dab1 T A 4: 104,570,987 (GRCm39) D210E Het
Elavl1 G A 8: 4,375,199 (GRCm39) probably benign Het
Emilin1 C T 5: 31,074,433 (GRCm39) Q225* probably null Het
Eml6 G T 11: 29,727,258 (GRCm39) A1288E probably benign Het
Eno1 T C 4: 150,329,796 (GRCm39) probably null Het
Eprs1 C T 1: 185,111,898 (GRCm39) R303C probably damaging Het
Eps15l1 G A 8: 73,126,878 (GRCm39) A651V probably benign Het
Etl4 A T 2: 20,714,368 (GRCm39) I156F probably damaging Het
Faim2 A T 15: 99,411,814 (GRCm39) I171N probably damaging Het
Fam135a T A 1: 24,069,939 (GRCm39) N381I probably damaging Het
Fhip1a G T 3: 85,637,831 (GRCm39) P156Q probably damaging Het
Gabrg3 T A 7: 56,384,833 (GRCm39) M243L probably benign Het
Garin2 A G 12: 78,761,809 (GRCm39) K158E possibly damaging Het
Gm5134 A G 10: 75,836,233 (GRCm39) I405V probably damaging Het
Gm9376 A T 14: 118,504,768 (GRCm39) K67* probably null Het
Grm8 A T 6: 27,761,354 (GRCm39) I290K possibly damaging Het
Hao1 T A 2: 134,390,121 (GRCm39) M73L probably benign Het
Herc1 A G 9: 66,369,150 (GRCm39) D452G Het
Idh3b C A 2: 130,123,413 (GRCm39) K192N possibly damaging Het
Igkv6-23 A G 6: 70,237,553 (GRCm39) S63P probably benign Het
Itgb2 A C 10: 77,384,398 (GRCm39) D173A probably damaging Het
Jmjd8 A T 17: 26,049,301 (GRCm39) T255S probably benign Het
Lamc3 A C 2: 31,820,714 (GRCm39) E1243A probably benign Het
Map1a A G 2: 121,129,939 (GRCm39) T252A probably damaging Het
Mrgpra1 C A 7: 46,985,203 (GRCm39) A159S probably benign Het
Ndst3 T C 3: 123,395,131 (GRCm39) I500V possibly damaging Het
Nhsl1 A G 10: 18,407,434 (GRCm39) T1523A possibly damaging Het
Nr2f1 A G 13: 78,343,298 (GRCm39) I322T probably damaging Het
Nup210 T C 6: 91,064,948 (GRCm39) E184G probably damaging Het
Obsl1 C T 1: 75,470,590 (GRCm39) W1022* probably null Het
Or2l13 T A 16: 19,306,449 (GRCm39) I287N probably damaging Het
Or4a77 T A 2: 89,486,846 (GRCm39) H313L probably benign Het
Or52p2 G T 7: 102,237,162 (GRCm39) Q263K possibly damaging Het
Or5p51 A T 7: 107,444,572 (GRCm39) Y123N probably damaging Het
Or6c1 A T 10: 129,518,149 (GRCm39) I153N probably damaging Het
Or6c65 T A 10: 129,603,720 (GRCm39) Y118* probably null Het
Otulinl A G 15: 27,658,319 (GRCm39) C184R probably benign Het
Oxr1 C T 15: 41,677,004 (GRCm39) P187L not run Het
Parp8 A G 13: 117,031,461 (GRCm39) L417P possibly damaging Het
Pdia6 A G 12: 17,324,509 (GRCm39) Q120R probably benign Het
Ppp3cc T C 14: 70,478,252 (GRCm39) N290S probably benign Het
Prdm5 C A 6: 65,808,244 (GRCm39) S63R possibly damaging Het
Prr14l T C 5: 32,988,445 (GRCm39) D350G probably benign Het
Pwwp2a T C 11: 43,607,878 (GRCm39) L497S probably damaging Het
R3hdm2 A G 10: 127,312,547 (GRCm39) N430D probably benign Het
Rad51ap2 A G 12: 11,507,344 (GRCm39) N422S possibly damaging Het
Rbbp8 G A 18: 11,805,638 (GRCm39) probably null Het
Rsf1 GGCGGCGGC GGCGGCGGCAGCGGCGGC 7: 97,229,125 (GRCm39) probably benign Het
Slc22a6 G A 19: 8,599,522 (GRCm39) probably null Het
Slc28a3 T A 13: 58,714,045 (GRCm39) E440V possibly damaging Het
Slc30a5 A T 13: 100,947,932 (GRCm39) I482K probably damaging Het
Slco1a1 A T 6: 141,870,223 (GRCm39) F305Y probably damaging Het
Slco1a8 G A 6: 141,938,220 (GRCm39) A253V probably damaging Het
Slco4c1 T C 1: 96,756,690 (GRCm39) N544S probably damaging Het
Spata31h1 A T 10: 82,120,953 (GRCm39) I4019K probably benign Het
Taok1 A T 11: 77,432,500 (GRCm39) L771* probably null Het
Tmem231 T C 8: 112,641,927 (GRCm39) D209G possibly damaging Het
Tmem25 A G 9: 44,706,705 (GRCm39) probably null Het
Tmem79 T C 3: 88,240,718 (GRCm39) T77A probably benign Het
Topbp1 A T 9: 103,205,836 (GRCm39) T825S probably damaging Het
Trpm6 A T 19: 18,853,455 (GRCm39) Q1825L probably benign Het
Uba1y T A Y: 821,348 (GRCm39) D110E probably damaging Het
Utrn A T 10: 12,261,280 (GRCm39) N3422K probably benign Het
Vmn1r219 A T 13: 23,347,314 (GRCm39) M168L probably benign Het
Vmn2r62 T C 7: 42,414,235 (GRCm39) H736R possibly damaging Het
Wdr1 T C 5: 38,697,435 (GRCm39) H291R possibly damaging Het
Zan T C 5: 137,413,401 (GRCm39) T3177A unknown Het
Zbtb21 T C 16: 97,752,495 (GRCm39) H596R possibly damaging Het
Other mutations in Smpd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00944:Smpd4 APN 16 17,460,621 (GRCm39) missense probably benign 0.04
IGL01461:Smpd4 APN 16 17,439,370 (GRCm39) missense probably damaging 1.00
IGL02051:Smpd4 APN 16 17,444,382 (GRCm39) missense probably damaging 1.00
IGL02492:Smpd4 APN 16 17,457,215 (GRCm39) missense probably damaging 1.00
IGL03181:Smpd4 APN 16 17,443,671 (GRCm39) nonsense probably null
Victim UTSW 16 17,458,835 (GRCm39) missense probably damaging 1.00
weakling UTSW 16 17,456,350 (GRCm39) intron probably benign
G1citation:Smpd4 UTSW 16 17,458,097 (GRCm39) missense probably damaging 1.00
R0197:Smpd4 UTSW 16 17,459,461 (GRCm39) critical splice donor site probably null
R0549:Smpd4 UTSW 16 17,457,176 (GRCm39) missense probably benign 0.15
R0789:Smpd4 UTSW 16 17,443,690 (GRCm39) missense probably benign 0.14
R1077:Smpd4 UTSW 16 17,441,833 (GRCm39) missense probably damaging 1.00
R1120:Smpd4 UTSW 16 17,456,350 (GRCm39) intron probably benign
R1716:Smpd4 UTSW 16 17,460,365 (GRCm39) missense probably damaging 1.00
R1758:Smpd4 UTSW 16 17,458,744 (GRCm39) missense probably damaging 1.00
R1758:Smpd4 UTSW 16 17,443,872 (GRCm39) missense probably damaging 0.99
R1838:Smpd4 UTSW 16 17,460,166 (GRCm39) splice site probably null
R2115:Smpd4 UTSW 16 17,444,729 (GRCm39) missense probably benign 0.33
R2849:Smpd4 UTSW 16 17,460,076 (GRCm39) missense probably damaging 1.00
R4654:Smpd4 UTSW 16 17,459,992 (GRCm39) intron probably benign
R6157:Smpd4 UTSW 16 17,458,930 (GRCm39) splice site probably null
R6190:Smpd4 UTSW 16 17,449,877 (GRCm39) missense probably damaging 1.00
R6822:Smpd4 UTSW 16 17,458,097 (GRCm39) missense probably damaging 1.00
R7062:Smpd4 UTSW 16 17,458,835 (GRCm39) missense probably damaging 1.00
R7759:Smpd4 UTSW 16 17,456,497 (GRCm39) missense probably damaging 1.00
R7853:Smpd4 UTSW 16 17,460,605 (GRCm39) missense probably damaging 1.00
R8187:Smpd4 UTSW 16 17,446,999 (GRCm39) missense probably damaging 1.00
R8303:Smpd4 UTSW 16 17,457,195 (GRCm39) missense probably damaging 1.00
R8518:Smpd4 UTSW 16 17,458,884 (GRCm39) missense possibly damaging 0.89
R8735:Smpd4 UTSW 16 17,453,410 (GRCm39) missense possibly damaging 0.92
R9075:Smpd4 UTSW 16 17,457,849 (GRCm39) missense unknown
R9439:Smpd4 UTSW 16 17,459,451 (GRCm39) missense probably benign
Z1176:Smpd4 UTSW 16 17,437,450 (GRCm39) intron probably benign
Z1177:Smpd4 UTSW 16 17,439,305 (GRCm39) critical splice acceptor site probably benign
Predicted Primers PCR Primer
(F):5'- CAGATATTCCGGGTATGTCCTG -3'
(R):5'- CTGGACAATGCCAGCATTTG -3'

Sequencing Primer
(F):5'- AGATATTCCGGGTATGTCCTGTACAG -3'
(R):5'- CTTGAGAAACGACAGCTC -3'
Posted On 2019-06-26